Catholic officials working to resettle Cuban refugees in this country yesterday disputed reports that thousands of homosexuals are among an estimated 40,000 Cubans still living in four refugee camps.

"We have people working in every camp, and to the best of our knowledge there are less than 700 homosexuals in the camps now," said George Wagner, assistant director of migration and refugees services for the U.S. Catholic Conference.

Wagner, who said his organization has resettled 60 to 70 percent of the more than 115,000 Cubans who came to the United States in the recent boatlift from Cuba's Mariel harbor to Key West, Fla., said he did not know how many homosexual refugees have been resettled, but thought the number to be minuscule.

National gay rights organizations and some federal sources have estimated that up to 20,000 of the refugees still awaiting sponsors are homosexuals.

However, spokesman for the Federal Emergency Management Agency, which has been coordinating resettlement efforts at the camps, now say that only 1,750 admitted homosexuals entered the United States in the boatlift.

But spokesmen for groups such as the Metropolitan Community Church, a nationwide gay-oriented organization, maintain that at least 10,000 homosexuals are still in the camps, and that at least twice that number were forced to leave Cuba in the boatlift.

The spokesmen say their figures are based on interviews with people in the camps.

"We've had estimates from as low as 4,000 to as many as 60,000," said John Donnelly, an official at the Community Church's Los Angeles head-quarters.

"The 60,000 figure may be a bit exaggerated. But our best information is that thousands of gays left Cuba and that thousands still remain within the camps," he said.

Justice Department and Immigration and Naturalization Service aides said yesterday they have no estimates on how many homosexuals entered as part of the boatlift.

Adding to the confusion is the opinion of some officials that many Cuban men lied and said they were homosexuals on their exit permits, in the hope that his would lead to their expulsion from Cuba.

On the other side, some gay groups contend that many refugees in the camps are refusing to admit that they are homosexuals because they fear that the United States will deport them if they do so.

U.S. Catholic Conference officials say that what they see as inflated estimates of the numbers of homosexual refugees are not only irresponsible, but are further hindering efforts to find sponsors for the Cubans.

But gay organization and newspapers contend that the government, the "established" media and some religious groups involved in the resettlement effort are deliberately underplaying the number of homosexuals who entered the country.

Miguel Martinez, a spokesman for the Cuban interest section here, said he could not comment on the conflicting numbers reports. "I can give you no information on that," he said.

And the Carter administration, criticized as having been duped by Cuban President Fidel Castro, is silent on the subject.